Health Facility Assessments (HFAs) assessing facilities’ readiness to provide services are well-established. However, HFA questionnaires are typically quantitative and lack depth to understand systems in which health facilities operate—crucial to designing context-oriented interventions. We report lessons from a multiple embedded case study exploring the experiences of HFA data collectors in implementing a novel HFA tool developed using systems thinking approach. We assessed 16 hospitals in four countries (Benin, Malawi, Tanzania, and Uganda) as part of a quality improvement implementation research. Our tool was organized in 17 sections and included dimensions of hospital governance, leadership, and financing; maternity care standards and procedures; ongoing quality improvement practices; interactions with communities; and mapping of the areas related to maternal care. Data for this study was collected using in-depth interviews with senior experts who conducted the HFA in the countries one to three months after completion of the HFAs. Data were analyzed using the inductive thematic analysis approach. Our HFA faced challenges in logistics (accessing key hospital-based respondents, high turnover of managerial staff, and difficulty accessing information considered sensitive in the context) and methodology (response bias, lack of data quality, and data entry into an electronic platform). Data elements of governance, leadership, and financing were the most affected. Opportunities and strategies adopted aimed at enhancing data collection (building on prior partnerships, understanding local and institutional bureaucracies) and enhancing data richness (identifying respondents with institutional memory, learning from experience, and conducting observations at various times). Moreover, HFA data collectors conducted abstraction of records and interviews in a flexible and adaptive way to enhance data quality. Lessons and new skills learned from our HFA could be used as inputs to respond to the growing need of integrating the systems thinking approach in HFA to improve contextual understanding of operations and structure.